The keystone species, Pisaster ochraceus, suffered mass mortalities along the northeast Pacific Ocean from Sea Star Wasting Syndrome (SSWS) outbreaks in 2013-2016. Causation of SSWS is still debated, leading to concerns as to whether outbreaks will continue to impact this species. Considering the apparent link between ocean temperature and SSWS, the future of this species and intertidal communities remains uncertain. We surveyed populations of sea stars along the Oregon coast in 2016, two years after the epidemic began. Cohabitation of asymptomatic and symptomatic individuals allowed us to ask whether lower susceptibility in asymptomatic individuals differed genetically. We performed restriction site-associated DNA sequencing (2bRAD-seq) to genotype thousands of single nucleotide polymorphism (SNP) loci. By comparing allele frequencies between symptomatic and asymptomatic individuals, we detected three loci that may be under selection. A multivariate analysis showed a clear separation between groups based on disease status in two of the three geographic regions, along with several regions across the genome having small statistical contributions to this separation. A draft annotation of protein-coding regions allowed us to identify 120 predicted genes that are linked to these markers and are putatively associated with lower susceptibility. Our results suggest that some variation in disease severity can be attributed to genetic variation. However, differences in phenotype have a highly polygenic nature with no single or few genomic regions having strong predictive effects. The genes associated with these regions may form the basis for functional studies aiming to understand disease progression in infected individuals.